A phylogenetic appraisal of Sigmodontinae (Rodentia,Cricetidae) with emphasis on phyllotine genera: systematics and biogeography

Here, we present a comprehensive phylogenetic analysis based on nuclear and mitochondrial DNA sequences of rodents of the subfamily Sigmodontinae. The emphasis is placed on the large tribe Phyllotini; sampling includes for the first time in any molecular‐based phylogenetic analysis representatives of several genera traditionally considered to be phyllotines. Given the broad taxonomic sampling, results provide substantial improvements in our knowledge on both the structure of the sigmodontine radiation and of phyllotine phylogenetic relationships. For instance, the tribe Ichthyomyini was not recovered monophyletic. Similarly, in a novel hypothesis on the contents of the tribe Phyllotini, it is shown that unlike Galenomys, the genera Chinchillula, Neotomys and Punomys are not phyllotines. The later genera together with Andinomys, Euneomys, Irenomys and Juliomys form part of novel generic clades of mostly Andean sigmodontine rodents. More in general, results strongly suggest the occurrence of several instances of putative morphological convergence among distinct sigmodontine lineages (e.g. among now considered to be ichthyomyines; between Phyllotini and some Andean taxa; among Euneomys‐Neotomys and Reithrodon). Finally, we suggest that the historical biogeography of the sigmodontine rodents is far more complex than earlier envisioned.     

Description of the karyotype of Rhagomys rufescens Thomas, 1886 (Rodentia, Sigmodontinae) from Southern Brazil Atlantic forest

Rhagomys rufescens (Rodentia: Sigmodontinae) is an endemic species of the Atlantic forest from Southern and Southeastern Brazil. Some authors consider Rhagomys as part of the tribe Thomasomyini; but its phylogenetic relationships remain unclear. Chromosomal studies on eight specimens of Rhagomys rufescens revealed a diploid number of 2n = 36 and a number of autosome arms FN = 50. GTG, CBG and Ag-NOR banding and CMA(3) /DAPI staining were performed on metaphase chromosomes. Eight biarmed and nine acrocentric pairs were found in the karyotype of this species. The X and Y chromosomes were both acrocentric. Most of the autosomes and the sex chromosomes showed positive C-bands in the pericentromeric region. The X chromosome showed an additional heterochromatic block in the proximal region of the long arm. Nucleolus organizer regions (NORs) were located in the pericentromeric region of three biarmed autosomes (pairs 4, 6 and 8) and in the telomeric region of the short arm of three acrocentrics (pairs 10, 12 and 17). CMA (3) /DAPI staining produced fluorescent signals in many autosomes, especially in pairs 4, 6, and 8. This study presents cytogenetic data of Rhagomys rufescens for the first time.     

Diversification of the climatic niche drove the recent processes of speciation in Sigmodontinae (Rodentia,Cricetidae)

Evolutionary radiations are among the most intriguing natural phenomena. Sigmodontine rodents form a megadiverse group for which doubts exist about the adaptive or non‐adaptive nature of its radiation. We analysed whether or not the rates of diversification of species of Sigmodontinae are related to the rates of diversification of the climatic niches occupied by the species. Our results show a clear association between niche diversification and speciation processes. However, this association is linked to recent and independent processes of diversification in sigmodontines, as opposed to an early link that would indicate a niche‐filling consistent with an adaptive radiation of the subfamily.     

Taxonomic review of genus Sooretamys Weksler,Percequillo & Voss (Rodentia: Cricetidae: Sigmodontinae): an integrative approach

Sooretamys is a monotypic genus of the family Cricetidae, subfamily Sigmodontinae, that is distributed throughout eastern South America in the Atlantic Forest Biome, including Argentina, Brazil, and Paraguay. The taxonomic history of the forms associated with this genus is long and relatively complex, and few studies have evaluated the taxonomic problems of this genus. To this end, our goal was to describe the degree and geographical pattern of morphological and molecular variation in this genus to test the current hypothesis that the genus is monotypic, and, as a consequence, to determine the status of the nominal forms associated with Sooretamys. Accordingly, we employed morphometric, morphological, and molecular tools, according to an integrative taxonomy approach. The results show that some level of morphometric discontinuity is present between the individuals from Paraguay and those from adjacent localities in Brazil and Argentina; sharp discontinuities were not observed in qualitative traits. Molecular analyses of the mitochondrial cytochrome b gene showed that the Paraguayan populations have some degree of genetic differentiation, but the haplotypic variants do not form a monophyletic group. Thus, the evidence so far suggests a difference in the genes and morphology of the Paraguayan population, but there is no consistent resolution (e.g. lack of monophyly) to show that specimens from Paraguay represent a distinct population that would merit taxonomic recognition. Thus, we recognize a single species within the genus Sooretamys, named Sooretamys angouya. The pattern of morphological and genetic differentiation of Sooretamys could be the result of divergence with gene flow. However, our data also correspond in some aspects with the model advanced by Carnaval & Moritz, which claims the existence of stable Atlantic Forest areas where the forest biota persisted during the Quaternary climatic fluctuations. Whatever process has occurred, S. angouya represents one species with a complex evolutionary history, and the analysis of additional samples would be welcome to further elucidate the process of diversification of this taxon. © 2014 The Linnean Society of London     

Revision of the taxonomic position of the Olkhon mountain vole (Rodentia,Cricetidae)

The phylogenetic position of the Olkhon mountain vole (Alticola olchonensis Litvinov, 1960) was studied using the sequences of four nuclear (BRCA, GHR, LCAT, and IRBP) and one mitochondrial (cyt. b) gene. Until now multiple studies of the systematic position of this vole had been based exclusively on morphological data, while the major taxonomic references contain contradictory information regarding both the subgeneric and species status of this animal. It was established that the molecular data and morphology data allow us to concern the Lake Baikal vole unambiguously as a part of the nominative subgenus Alticola instead of Aschizomys.     

First phylogenetic analysis of the tribe Phyllotini (Rodentia: Sigmodontinae) combining morphological and molecular data

Previous phylogenetic analyses of the tribe Phyllotini, one of the largest components of the subfamily Sigmodontinae, have been based on a single source of evidence. In particular, morphological analyses were largely based on craniodental data, almost neglecting the potential phylogenetic information present in the postcranium. Despite the significant advances made in relation to the knowledge of phyllotine phylogeny in recent times, there are several unsolved issues that highlight the importance of a phylogenetic analysis that integrates multiple sources of evidence, including previously considered sources as well as new sources of data. We present here the first combined phylogenetic analysis (morphological and molecular) of phyllotines, which includes the widest taxon and character sampling to date. Our dataset includes 164 morphological characters, of which 83 are postcranial characters, plus 3561 molecular characters, scored for 52 species from 34 genera of Oryzomyalia. In this study 75 postcranial characters not previously considered in this group are thoroughly described, and their utility for solving the relationships within Phyllotini is evaluated by means of different complementary analyses. Phyllotini was retrieved as a monophyletic clade in the combined analysis, with a composition that matches that obtained in most other recent analyses. All genera of phyllotines were monophyletic and show high support values. Abrotrichini, Akodontini and Oryzomyini were also monophyletic. The inclusion of postcranial data appears to be of limited utility to solve the phylogenetic relationships within Phyllotini.     

Geographic distribution and phenetic skull variation in two close species of Graomys (Rodentia, Cricetidae, Sigmodontinae)

The interspecific differentiation of South American rodents of the genus Graomys was assayed at ecological and morphometric levels in two species. At the ecological level, niche modelling was used. At the morphometric level, the hypothesis that the size and shape of the skull vary with the geographic location was tested using geometric morphometrics by assessing the extent and spatial distribution of phenotypic skull variation within and among two species, Graomys griseoflavus and Graomys chacoensis. Our results of niche modelling indicate the spatial differentiation between the two species, with G. chacoensis inhabiting preferably the Chaco ecoregion and G. griseoflavus inhabiting mainly the Monte ecoregion. In multiple linear regressions, approximately 20% of the skull size variation is explained by latitude, altitude, and temperature seasonality. The partial least square analysis reveals strong correlation between shape and environmental variables, mainly with latitude, annual mean temperature, and annual precipitation. Discrimination between G. griseoflavus and G. chacoensis was highly reliable when using geometric morphometric tools. These results permit us to elucidate some evolutionary processes that have occurred in these species.     

A new record and an evaluation of the phylogenetic relationships of Abrothrix olivaceus markhami (Rodentia: Sigmodontinae)

Recent phylogenetic studies of the subfamily of cricetid rodents (Sigmodntinae) have validated the taxonomic classification at the tribal level of the Andean Clade. It is possible that some endemic species from Patagonian South America are part of this new tribe, but previous studies have not evaluated this hypothesis due to the difficulty of obtaining samples. In this study, we evaluate the phylogenetic relationships of Akodon markhami (Pine, 1973), a species endemic to the Chilean Patagonia, using individuals recently captured at the type locality of this taxon. Our results indicate that this form of Akodon corresponds to a subspecies of Abrothrix olivaceus, and should be incorporated into the Andean Clade as a geographic race of this widely distributed species on the South American continent. Based on a molecular clock calibration, we dated the origin of this geographic race during the last glacial cycles of the Quaternary, as the result of a vicariant process.     

Genome analysis of Peromyscus (Rodentia,Cricetidae)

A satellite DNA fraction from P. eremicus, having a buoyant density of 1.705 g/ml in neutral CsCl density gradients, was isolated. In situ hybridization experiments, using 3H-RNA complementary to this DNA fraction indicated that the short (heterochromatic) arms of most of the autosomes contained this sequence. Conversely, in situ hybridization using 3H-complementary DNA (cDNA) synthesized from the cytoplasmic poly (A) RNA of P. eremicus (comprising a substantial fraction of total messenger RNA) showed that the number of silver grains in the long arms (euchromatin) was significantly higher than that in the short arms. The X chromosomes showed a distinct localization pattern of both sequences.     

A multilocus perspective on the phylogenetic relationships and diversification of rodents of the tribe Abrotrichini (Cricetidae: Sigmodontinae)

Abrotrichini is a recently defined and diagnosed tribe of Sigmodontinae with a complex taxonomy. Abrotrichine genera, Abrothrix (including Chroeomys), Chelemys, Geoxus, Notiomys and Pearsonomys, are mostly distributed in the central and southern Andes and adjacent lowlands and show terrestrial and fossorial habits. Recent studies have evidenced some incongruence between current taxonomy and abrotrichine phylogeny, such as the polyphyly of Chelemys and paraphyly of Geoxus respect to Pearsonomys. We used DNA sequence data of six loci (one mitochondrial and five nuclear) to resolve the relationships within the tribe. Independent and combined analyses of these loci were carried out using parsimony, maximum likelihood and Bayesian inference. Estimates of divergence time of the main lineages of abrotrichines were calculated with a molecular clock using as calibration, a fossil recently found. The concatenated data set increased the resolution and defined the relationships within the tribe. Our phylogenetic analyses corroborate that Abrothrix is sister of a clade containing the long‐clawed abrotrichines. We recovered two main clades within Abrothrix that match morphologic variation and geographic distribution of its species. In addition, we corroborated the lack of monophyly of Chelemys and the lack of monophyly of Geoxus. We discuss different taxonomic scenarios to abrotrichine classification reflects the phylogenetic relationships obtained in this study. Our molecular clock estimated the Abrotrichini crown age to be around the early Pliocene (4.4 Ma) and suggest that the tribe diversified over a short period of time.     

中国森林田鼠族系统分类研究进展(啮齿目:仓鼠科:䶄亚科)

森林田鼠族（Myodini）是䶄亚科（Arvicolinae）的重要类群,广泛分布于整个全北区及东洋区部分区域,该族目前存在的分类学问题是缺乏化石标本、短时间的物种分化、有限分子样本和部分类群采样困难等综合因素影响的结果。近年中国森林田鼠族的系统分类研究成果主要有：（1）绒鼠属（Eothenomys）的采样和系统发育研究基本涵盖了全部类群,发现1新亚属和4新种,分别为川西绒鼠亚属（Ermites）和石棉绒鼠（Eothenomys shimianensis）、金阳绒鼠（E.jinyangensis）、美姑绒鼠（E.meiguensis）、螺髻山绒鼠（E.luojishanensis）,原来被普遍接受的黑腹绒鼠福建亚种（E.melanogaster colurnus）、中华绒鼠康定亚种（E.chinensis tarquinius）、西南绒鼠康定亚种（E.custos hintoni）被证实为3个独立有效种,滇绒鼠（E.eleusis）、丽江绒鼠（E.fidelis）的种级分类地位进一步得到确认;大绒鼠贡山亚种（E.miletus confinii）和黑腹绒鼠滇西亚种（E.melanogaster libonotus）实为克钦绒鼠（E.cachinus）的同物异名。（2）基于形态和分子系统发育的研究支持恢复东亚䶄属（Craseomys）的属级分类地位,同时解决了䶄属（Myodes）的非单系起源问题;研究进一步证实山西䶄（Craseomys shanseius）应为棕背䶄的山西亚种（Craseomys rufocanus shanseius）。（3）高山䶄属（Alticola）的平颅高山䶄亚属（Platycranius）分类地位受到分子系统发育研究结果质疑,该亚属的唯一物种平颅高山䶄（Alticola strelzowi）与高山䶄属指名亚属物种聚在同一枝;库蒙高山䶄（A.stracheyi）实为斯氏高山䶄（A.stoliczkanus）的同物异名。基于近年系统分类研究结果,目前中国森林田鼠族分布有5属共30种。     

Evolution of the genome size inAkodon (Rodentia,Cricetidae)

Nuclear DNA contents were estimated by microdensitometry in five species of Akodon rodents: Arodon molinae, A. dolores, A. mollis, A. azarae, Bolomys obscurus) and in three chromosomal varieties of A. molinae (2n = 42; 2n = 43, 2n = 22). The data obtained showed that the species with the highest DNA content was B. obscurus, followed in order of decreasing genome size by A. molinae, A. mollis, A. dolores and A. azarae. In A. molinae the forms with 2n = 42 chromosomes had the lowest and the forms with 2n = 44 the highest amount of DNA, while the forms with 2n = 43 had intermediate DNA contents. The variation in DNA amount detected in A. molinae was interpreted as a phenomenon of amplification occurring in the chromosomal areas involved in the chromosomal rearrangement giving rise to the polymorphism exhibited by this species. The DNA contents of shared chromosomes (chromosomes with similar size, morphology and G banding pattern, which are found in two or more phylogenetically related species), were compared and correlated with values of total nuclear DNA. The information obtained indicates that: (a) shared chromosomes have variable amounts of DNA: (b) in a given species there is a correlation between the amount of nuclear and chromosomal DNA in most shared chromosomes (and perhaps in most of the chromosomal complement), e.g., the higher the amount of nuclear DNA, the higher the content of DNA in shared chromosomes; (c) some chromosomes may undergo processes of amplification or deletion restricted to certain regions and usually related with mechanisms of chromosomal rearrangements.(ABSTRACT TRUNCATED AT 250 WORDS)     

Systematics of the southern Patagonian-Fueguian endemic Abrothrix lanosus (Rodentia: Sigmodontinae): Phylogenetic position,karyotypic and morphological data

Abrothrix lanosus (Thomas, 1897) is morphologically redescribed on the basis of new specimens collected in Tierra del Fuego (Argentina). Cranial, mandibular, skeletal, penile, and chromosomal characteristics are described and compared with other species of Abrothrix, especially those of the Patagonian-Fueguian region. Its phylogenetic position within Abrotrichini is explored using DNA sequences of the mitochondrial cytochrome b (cyt b) and the nuclear Interphotoreceptor Retinoid Binding Protein (IRBP) genes. Phylogenetically, cyt b places A. lanosus as sister of A. jelskii, whereas IRBP groups A. lanosus and A. longipilis. The latter topology is most consistent with morphological data and taxonomic history. Several cranial and mandibular characters distinguish A. lanosus from the other species of the genus, including A. longipilis, which is its most similar species. A. lanosus shares with other congeners a 2n=52 karyotype and differs from other species of Abrothrix by at least 10% (p-distances) sequence divergence in cyt b. In conclusion, A. lanosus is a valid species, readily distinguishable from other Abrothrix in the southern Patagonian-Fueguian region. Although many data, including penile and skull morphology, suggest that A. longipilis is its closest living relative, A. jelskii is retained as a viable alternative until additional data are obtained.     

Dating an impressive Neotropical radiation: Molecular time estimates for the Sigmodontinae (Rodentia) provide insights into its historical biogeography

With about 400 living species and 82 genera, rodents of the subfamily Sigmodontinae comprise one of the most diverse and more broadly distributed Neotropical mammalian clades. There has been much debate on the origin of the lineage or the lineages of sigmodontines that entered South America, the timing of entrance and different aspects of further diversification within South America. The ages of divergence of the main lineages and the crown age of the subfamily were estimated by using sequences of the interphotoreceptor retinoid binding protein and cytochrome b genes for a dense sigmodontine and muroid sampling. Bayesian inference using three fossil calibration points and a relaxed molecular clock estimated a middle Miocene origin for Sigmodontinae (～12 Ma), with most tribes diversifying throughout the Late Miocene (6.9–9.4 Ma). These estimates together results of analyses of ancestral area reconstructions suggest a distribution for the most recent common ancestor of Sigmodontinae in Central-South America and a South American distribution for the most recent common ancestor of Oryzomyalia.     

Integrative taxonomy, systematics and distribution of the genus Eligmodontia (Rodentia, Cricetidae, Sigmodontinae) in the temperate Monte Desert of Argentina

The systematics and distribution of South American sigmodontine rodents a matter of continuous revision and debate. The silky mice, genus Eligmodontia Cuvier, 1837, are among the most specialized murid rodents endemic to South America and its diversification for desert existence is associated with the uplift of the Andes and the early development of arid landscapes. Aiming to clarify the systematics of the species of silky mice occurring in the driest portion of the temperate Monte Desert in Argentina, qualitative and quantitative external and cranial characters, cytogenetics and molecular relationships, were studied. We characterized three karyotypes of Eligmodontia; two of which are described for the first time, and allocated them to previously named species. E. moreni Thomas, 1896 (2n=52 and FN=50), E. typus Cuvier, 1837 (2n=44 and FN=44) and E. marica Thomas, 1918. The later shows the same diploid number of E. typus, but its X—chromosome is not METACENTRIC but ACROCENTRIC . A discriminant analysis of external and cranial data separates E. moreni from E. typus and E. marica. Whereas these last ones show some degree of overlap. The morphological and chromosomal differentiation of Eligmodontia is sustained by DNA distances. Phylogenetic analyses show two major clades. One formed by E. moreni, E. puerulus and E. hirtipes, sharing a high FN and a northern distribution, and THE other formed by E. typus, E. marica and E. morgani with low FN and a central-southern distribution. Two centers of diversification are proposed to explain the evolution of Eligmodontia.